neurom¶

NeuroM top level module

Examples

Load a neuron

>>> import neurom as nm
>>> nrn = nm.load_neuron('some/data/path/morph_file.swc')

Obtain some morphometrics

>>> ap_seg_len = nm.get('segment_lengths', nrn, neurite_type=nm.APICAL_DENDRITE)
>>> ax_sec_len = nm.get('section_lengths', nrn, neurite_type=nm.AXON)

Load neurons from a directory. This loads all SWC, HDF5 or NeuroLucida .asc files it finds and returns a list of neurons

>>> import numpy as np  # For mean value calculation
>>> nrns = nm.load_neurons('some/data/directory')
>>> for nrn in nrns:
...     print 'mean section length', np.mean(nm.get('section_lengths', nrn))

Functions

`get`	Obtain a feature from a set of morphology objects
`iter_neurites`	Iterator to a neurite, neuron or neuron population
`load_neuron`	Build section trees from an h5 or swc file

Classes

NeuriteType Enum representing valid tree types